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If I am converting a video file (using any number of suites, currently VirtualDub), what's the best way to keep the audio in sync with the video?

You need to be WAY more specific. There are so many combinations of source media, codecs, filters, muxers, container formats, etc that it's pretty much impossible to offer a solution that's guaranteed to fix your problem, or even be suitable to the particular conversion you're performing.

Describe the specific problem you're having - tell us everything - and maybe someone can provide a useful response.

I can elaborate more, but to put it simply, I just don't have the magic touch it takes to get things into sync.

Here's a good example. I have an XviD AVI file that is encoded in AC3. It won't play on my media player. I know that the problem is the audio because I can strip it out and get the video to play. So... I know I need to change the audio.

I've tried Xilisoft Video Converter and, VirtualDub to try and convert the audio to Lame MP3. I've tried some of the PS3/PSP Video 9 suites to convert to MP4. Every time I do anything, I always end up with out of sync audio. Surely there has to be an easy way to fix this, right?

I have experienced VirtualDub throwing off audio sync on one particular type of file (Dish Network H.264 fed in through an AviSynth script, using DirectShowSource() and CoreCodec). Feeding that same AviSynth script into ffmpeg maintained audio sync. Go figure.

I have experienced VirtualDub throwing off audio sync on one particular type of file (Dish Network H.264 fed in through an AviSynth script, using DirectShowSource() and CoreCodec). Feeding that same AviSynth script into ffmpeg maintained audio sync. Go figure.

Tried that... The video will no longer load up in WM11.

EDIT: Nevermind. My codecs are scrambled. I will reattempt the conversion and report back.

If ffpmeg isn't working, maybe try an mencoder based solution. Format Factory is a GUI front end for a well configured mencoder system. However, don't use the newest version (1.65) as it has issues, use 1.55. Just be sure to set the fps to match, and choose a custom configuration in order to set custom resolutions/bitrates.